Job ID = 4178429 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 554,338 reads read : 1,108,676 reads written : 1,108,676 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:54 554338 reads; of these: 554338 (100.00%) were paired; of these: 95461 (17.22%) aligned concordantly 0 times 388050 (70.00%) aligned concordantly exactly 1 time 70827 (12.78%) aligned concordantly >1 times ---- 95461 pairs aligned concordantly 0 times; of these: 36112 (37.83%) aligned discordantly 1 time ---- 59349 pairs aligned 0 times concordantly or discordantly; of these: 118698 mates make up the pairs; of these: 82510 (69.51%) aligned 0 times 21688 (18.27%) aligned exactly 1 time 14500 (12.22%) aligned >1 times 92.56% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 6125 / 394239 = 0.0155 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:21:21: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:21:21: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:21:29: 1000000 INFO @ Thu, 05 Dec 2019 12:21:29: #1 tag size is determined as 74 bps INFO @ Thu, 05 Dec 2019 12:21:29: #1 tag size = 74 INFO @ Thu, 05 Dec 2019 12:21:29: #1 total tags in treatment: 453085 INFO @ Thu, 05 Dec 2019 12:21:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:21:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:21:29: #1 tags after filtering in treatment: 448078 INFO @ Thu, 05 Dec 2019 12:21:29: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:21:29: #1 finished! INFO @ Thu, 05 Dec 2019 12:21:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:21:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:21:29: #2 number of paired peaks: 147 WARNING @ Thu, 05 Dec 2019 12:21:29: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 05 Dec 2019 12:21:29: start model_add_line... INFO @ Thu, 05 Dec 2019 12:21:29: start X-correlation... INFO @ Thu, 05 Dec 2019 12:21:29: end of X-cor INFO @ Thu, 05 Dec 2019 12:21:29: #2 finished! INFO @ Thu, 05 Dec 2019 12:21:29: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 12:21:29: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 05 Dec 2019 12:21:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05_model.r WARNING @ Thu, 05 Dec 2019 12:21:34: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:21:34: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 05 Dec 2019 12:21:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:21:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:21:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.05_summits.bed INFO @ Thu, 05 Dec 2019 12:21:35: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:21:50: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:21:50: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:21:58: 1000000 INFO @ Thu, 05 Dec 2019 12:21:58: #1 tag size is determined as 74 bps INFO @ Thu, 05 Dec 2019 12:21:58: #1 tag size = 74 INFO @ Thu, 05 Dec 2019 12:21:58: #1 total tags in treatment: 453085 INFO @ Thu, 05 Dec 2019 12:21:58: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:21:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:21:58: #1 tags after filtering in treatment: 448078 INFO @ Thu, 05 Dec 2019 12:21:58: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:21:58: #1 finished! INFO @ Thu, 05 Dec 2019 12:21:58: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:21:58: #2 number of paired peaks: 147 WARNING @ Thu, 05 Dec 2019 12:21:58: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 05 Dec 2019 12:21:58: start model_add_line... INFO @ Thu, 05 Dec 2019 12:21:58: start X-correlation... INFO @ Thu, 05 Dec 2019 12:21:58: end of X-cor INFO @ Thu, 05 Dec 2019 12:21:58: #2 finished! INFO @ Thu, 05 Dec 2019 12:21:58: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 12:21:58: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 05 Dec 2019 12:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10_model.r WARNING @ Thu, 05 Dec 2019 12:21:58: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:21:58: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 05 Dec 2019 12:21:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:21:58: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:21:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.10_summits.bed INFO @ Thu, 05 Dec 2019 12:21:59: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (48 records, 4 fields): 48 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:22:20: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:22:20: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:22:28: 1000000 INFO @ Thu, 05 Dec 2019 12:22:28: #1 tag size is determined as 74 bps INFO @ Thu, 05 Dec 2019 12:22:28: #1 tag size = 74 INFO @ Thu, 05 Dec 2019 12:22:28: #1 total tags in treatment: 453085 INFO @ Thu, 05 Dec 2019 12:22:28: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:22:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:22:28: #1 tags after filtering in treatment: 448078 INFO @ Thu, 05 Dec 2019 12:22:28: #1 Redundant rate of treatment: 0.01 INFO @ Thu, 05 Dec 2019 12:22:28: #1 finished! INFO @ Thu, 05 Dec 2019 12:22:28: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:22:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:22:28: #2 number of paired peaks: 147 WARNING @ Thu, 05 Dec 2019 12:22:28: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Thu, 05 Dec 2019 12:22:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:22:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:22:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:22:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:22:28: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 12:22:28: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 05 Dec 2019 12:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20_model.r WARNING @ Thu, 05 Dec 2019 12:22:28: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:22:28: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 05 Dec 2019 12:22:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:22:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:22:29: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3434310/SRX3434310.20_summits.bed INFO @ Thu, 05 Dec 2019 12:22:29: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。